I've got each position carried out to 32 slots for a project that I don't believe fits this space, so I'll just include the top 25 here. I'll also include last player out. For some players, it's hard to slot them at a particular position (where does King Kelly go, for example) so I just chose one (if you don't see a first baseman in the top 25 who you know should be there, maybe he's a third baseman instead).
Each player is only listed with one team - the team that is most representative of his MLB performance. This is just merit, that's the only way I rank stuff - it's not social impact or the quality of their character. It's performance.
1. Honus Wagner (1897-17, Pirates) WAR 130.95 OPS+151, PA 11749 (WAR/PA .0111) EMVPQ: 08 MVPQ: 05, 06, 09, 07, 12,
2. Alex Rodriguez (1994-16. Yankees) WAR 123.7 OPS+140 PA 12207 (.0101) EMVPQ: 00, MVPQ: 07, 96, 05, 02, 98, 03, 01,
3. Cal Ripken (1981-01, Orioles) WAR 105.6 OPS+112 PA 12883 (.0082) EMVPQ: 84, 91 MVPQ: 83,
4. Arky Vaughan (1932-48, Pirates) WAR 76.2, OPS+ 136 PA 7722 (99) MVPQ: 35,
5. Barry Larkin (1986-04, Reds) WAR 76.1, OPS+116 PA 9057 (84)
6. Ozzie Smith (1978-96, Cardinals) WAR 82.3, OPS+ 87 PA 10778 (76)
7. Robin Yount (1974-93, Brewers) WAR 81.8 OPS+ 115 PA 12249 (67) EMVPQ: 82
8. Alan Trammell (1977-96, Tigers) WAR 78.35, OPS+110 PA 9396 (83) MVPQ: 97,
9. Derek Jeter (1995-2014, Yankees) WAR 74.5 OPS+115 PA 12602 (59)
10. George Davis (1890-09, Giants) WAR 78.5, OPS+ 121 PA 10178 (77)
11. Bill Dahlen (1891-1911, Colts) WAR 78.1 OPS+110 PA 10405 (75)
12. Lou Boudreau (1938-52, Indians) WAR 63.65 OPS+120 PA 7024 (91) EMVPQ: 48,
13. Joe Cronin (1926-45, Red Sox) WAR 67.7 OPS+119 PA 8840 (77) MVPQ: 30,
14. Luke Appling (1930-50, White Sox) WAR 72.3 OPS+ 113 PA 10254 (71)
15. Pee Wee Reese (1940-58, Dodgers) WAR 64.1 OPS+99 PA 9470 (68)
16. Ernie Banks (1953-71, Cubs) WAR 62.75 OPS+ 122 PA 10394 (60) EMVPQ: 59 MVPQ: 58, 55, 60
17. Jack Glasscock (1879-95, Blues) WAR 63.35, OPS+112 PA 7552 (84)
18. Bobby Wallace (1894-1918, Browns) WAR 64.65 OPS+ 105 PA 9612 (67) MVPQ: 01
19. Troy Tulowitzki (2006-, Rockies) WAR 50.75 OPS+118 PA 5402 (94) MVPQ: 07
20. Nomar Garciaparra (1996-09, Red Sox) WAR 49.95 OPS+ 124 PA 6116 (82) MVPQ: 00,
21. Joe Sewell (1920-33, Indians) WAR 53.6 OPS+ 108 PA 8333 (64) MVPQ: 23
22. Tony Fernandez (1983-01, Jays) WAR 56.2 OPS+ 101 PA 8793 (64)
23. Miguel Tejada (1997-13, A’s) 54.85 OPS+ 108 PA 9205 (60) MVPQ: 04
24. Art Fletcher (1909-22, Giants) WAR 46.75 OPS+ 100 PA 6036 (77)
25. Joe Tinker (1902-16, Cubs) WAR 49.75 OPS+ 96 PA 7153 (70)
(last out - Monte Ward)